Various analytical instruments can be used for analyzing peptides, proteins, and other biomolecules. Mass spectrometry has gained prominence because of its ability to handle a wide variety of biomolecules with high sensitivity and rapid throughput. For example, proteins can be identified via analysis of spectra acquired using a tandem mass spectrometer. In some instances, the proteins are initially digested using a proteolytic agent to produce a variety of peptides, and the peptides are then analyzed by the tandem mass spectrometer to acquire a series of spectra.
In some instances, a tandem mass spectrometer is coupled to a chromatography system to analyze biomolecules present in a sample stream. For example, successive eluting portions of the sample stream can flow from a chromatography column, such as a High Performance Liquid Chromatography (“HPLC”) column, into the tandem mass spectrometer, and a series of spectra can be acquired from the eluting portions. While coupling of the tandem mass spectrometer to the chromatography system is desirable for a variety of reasons, such a configuration presents challenges in terms of efficiency at which mass spectrometry data can be acquired during a particular chromatography run. For example, based on analyzing a spectrum acquired from a particular eluting portion of a sample stream, it can be desirable to acquire additional spectra from that same eluting portion. However, the rate of elution of biomolecules present in the sample stream can be too fast for effective manual control of the tandem mass spectrometer. Also, it can be undesirable or impractical to interrupt a flow of the sample stream. In addition, there might be insufficient material for repeated analysis.